Chipotle's chicken burrito currently costs $7.81 in New York. A 5% increase would raise the price to about $8.20.

Ells said that the company is going to start charging more as it eliminates Genetically Modified Organisms from its ingredients:

"I think that (the price increase is) probably in kind of a mid-single digit range, whether that’s 3, 4, 5 kind of percent. What it will depend on is what happens with general ingredient inflation between now and then and then what it costs us to remove GMOs from the rest of our ingredients. Once we have all that information at hand we’ll be able to do a better job of figuring out what the price increase might be."

Activists have said that GMOs might not be as safe as natural foods because they have been altered from their natural states.

Ells said he hopes to time Chipotle's price increase around the elimination of GMOs.

"We are not aware of any other restaurant company anywhere near our sight that’s even attempting to do this and so to actually accomplish it will be pretty exciting and we’d like to time that excitement around with the price increase," Ells said.